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Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
Open accessAbstract
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA 'baits' to fish targets out of a 'pond' of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that approximately 60% of target bases in the exonic 'catch', and approximately 80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.
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“In genome research, an average depth of sequence coverage of 30-fold has been accepted as sufficient for single-nucleotide polymorphism (SNP) and nucleotide insertion or deletion (indel) detection (15–22).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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“Target capture and next-generation sequencing (NGS) have shown efficacy and, recently, scalability for resequencing human genomes and exomes, providing an alternative potential paradigm for comprehensive carrier testing (15–22).”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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“Preliminary experiments suggested that existing protocols for Agilent SureSelect hybrid capture (15) and RainDance microdroplet polymerase chain reaction (PCR) (16) but not Febit HybSelect microarray-based biochip capture (30) or Olink padlock probe ligation and PCR (31) yielded consistent target enrichment.”
From Carrier testing for severe childhood recessive diseases by next-generation sequencing (2011) · cites this paper as [15]
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Scherz, M. D., Rasolonjatovo, S. M., Köhler, J., Rancilhac, L., Rakotoarison, A., Raselimanana, A. P., Ohler, A., Preick, M., Hofreiter, M., Glaw, F., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-75431-9 · Cited by 26
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Self-citationA probabilistic approach for SNP discovery in high-throughput human resequencing dataPreprint
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Chromosome genomics uncovers plant genome organization and function
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Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review
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“Over the years, this method has been modified where biotin-labeled oligonucleotides are used and retrieved using streptavidin beads, hence the solution-based hybridization [39,40].”
MethodPhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification
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“Most efficient methods rely on the complementary hybridization of oligonucleotide capture probes to the targeted DNA sequences; these methods use capture arrays (31–33), or solution phase, also known as solution hybridization selection (3, 34, 35).”
Mullen, M. P., Creevey, C. J., Berry, D. P., McCabe, M. S., Magee, D. A., Howard, D. J., Killeen, A. P., Park, S. D., McGettigan, P., Lucy, M., et al. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-16 · Cited by 24
Sekelja, M., Paulsen, J., & Collas, P. (2016) · Genome biology · doi:10.1186/s13059-016-0923-2 · Cited by 26
“Additionally, capture arrays can be used to increase resolution for selected loci [63, 64] at the expense of compromising full-genome reconstruction.”
BackgroundMolecular and Functional Characterization of a Cohort of Spanish Patients with Ataxia-Telangiectasia
Carranza, D., Vega, A. K., Torres‐Rusillo, S., Montero-Mateos, E., Martínez-González, L. J., Santamaria, M. L., Santos, J. L., & Molina, I. J. (2016) · NeuroMolecular Medicine · doi:10.1007/s12017-016-8440-8 · Cited by 24
“This procedure allows the capture of the gene of interest whereby only the targeted area will be sequenced (Gnirke et al. 2009).”
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Vitiello, P. P., Rousseau, B., Chilà, R., Battuello, P., Amodio, V., Battaglieri, V., Grasso, G., Scardellato, S., Anselmo, A., Clemente, F., et al. (2025) · Cancer Cell · doi:10.1016/j.ccell.2025.05.014 · Cited by 26
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Improving ancient DNA genome assembly
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Familial cortical myoclonus with a mutation in NOL3
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Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization
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New technologies in the genetic approach to sudden cardiac death in the young
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BRCA-associated protein 1 mutant cholangiocarcinoma: an aggressive disease subtype
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“Sequence data from genomic DNA were mapped onto the reference human genome (hg19) using the Burrows-Wheeler Aligner and processed using the opensource packages SAMtools, Picard, and Genome Analysis Toolkit (8,9).”
MethodGlenn, T. C., & Faircloth, B. C. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12574 · Cited by 24
“…RNA baits (also called probes) to target DNA regions, physically pulls down the targeted DNA regions of interest and washes away unwanted DNA fragments so that the targeted DNA can be sequenced (Karagyozov et al. 1993; Kandpal et al. 1994; Albert et al. 2007; Okou et al. 2007; Gnirke et al. 2009).”
BackgroundInfluentialMassive Parallel Regression: A Précis of Genetic Mechanisms for Vision Loss in Diving Beetles
Tierney, S. M., Langille, B. L., Humphreys, W. F., Austin, A. D., & Cooper, S. J. (2018) · Integrative and Comparative Biology · doi:10.1093/icb/icy035 · Cited by 23
Barrow, L. N., Allen, J. M., Huang, X., Bensch, S., & Witt, C. C. (2018) · Molecular Ecology Resources · doi:10.1111/1755-0998.12977 · Cited by 23
Genomic resources for the Neotropical tree genus Cedrela (Meliaceae) and its relatives
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Evolution of Lomandroideae: Multiple origins of polyploidy and biome occupancy in Australia
Gunn, B. F., Murphy, D. J., Walsh, N. G., Conran, J. G., Pires, J. C., Macfarlane, T. D., & Birch, J. L. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106836 · Cited by 23
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Capturing prokaryotic dark matter genomes
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“Gene capture approaches, which were first developed for resequencing application, rely on either solid phase [1,123,138] or solution phase hybridization [65,182] of nucleic acid capture probes to the targeted DNA sequences.”
BackgroundTargeted sequencing of the human X chromosome exome
Mondal, K., Shetty, A. C., Patel, V., Cutler, D. J., & Zwick, M. E. (2011) · Genomics · doi:10.1016/j.ygeno.2011.04.004 · Cited by 22
The Genomic Era of Clinical Oncology: Integrated Genomic Analysis for Precision Cancer Care
Surrey, L. F., Luo, M., Chang, F., & Li, M. M. (2016) · Cytogenetic and Genome Research · doi:10.1159/000454655 · Cited by 22
“, 2007] or a solution-based method, in which biotinylated probes complementary to the ROIs are used to bind targets, which are then purified using streptavidin-labeled magnetic beads [Gnirke et al., 2009].”
MethodPanzera, A., Leaché, A. D., D’Elía, G., & Victoriano, P. F. (2017) · PeerJ · doi:10.7717/peerj.3941 · Cited by 22
“…short probes (60–120 base pairs) to hybridize to specific genomic regions, which are then isolated and sequenced using next-generation sequencing (Gnirke et al., 2009; McCormack et al., 2012), a method successfully used to resolve relationships among mammals (McCormack et al., 2012), birds…”
InfluentialRibeiro, P. G., Jiménez, M. F. T., Andermann, T., Antonelli, A., Bacon, C. D., & Matos‐Maraví, P. F. (2021) · Molecular Ecology · doi:10.1111/mec.16240 · Cited by 22
“Loci of interest are often enriched in the laboratory prior to sequencing (in vitro enrichment; Albert et al., 2007; Gnirke et al., 2009) to achieve a sufficiently high read coverage for its processing into multilocus data sets.”
BackgroundAdvances in sarcoma molecular diagnostics
Wang, X. Q., Goytain, A., Dickson, B. C., & Nielsen, T. O. (2022) · Genes Chromosomes and Cancer · doi:10.1002/gcc.23025 · Cited by 22
Benefits and Limits of Phasing Alleles for Network Inference of Allopolyploid Complexes
Tiley, G. P., Crowl, A. A., Manos, P. S., Sessa, E. B., Solís‐Lemus, C., Yoder, A. D., & Burleigh, J. G. (2024) · Systematic Biology · doi:10.1093/sysbio/syae024 · Cited by 22
Applications of Next-Generation Sequencing to Blood and Marrow Transplantation
Chapman, M., Warren, E. H., & Wu, C. J. (2012) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2011.11.011 · Cited by 22
Next-generation sequencing approaches for genetic mapping of complex diseases
Casals, F., Idaghdour, Y., Hussin, J., & Awadalla, P. (2012) · Journal of Neuroimmunology · doi:10.1016/j.jneuroim.2011.12.017 · Cited by 26
“rare variants associated to the disease (Druley et al., 2009; Gnirke et al., 2009; Out et al., 2009; Wang et al., 2010b; Bansal et al., 2011).”
Schiemann, A. H., Dürholt, E. M., Pollock, N., & Stowell, K. M. (2012) · British Journal of Anaesthesia · doi:10.1093/bja/aes341 · Cited by 22
Sánchez-Barreiro, F., Vieira, F. G., Martin, M. D., Haile, J., Gilbert, M. T. P., & Wales, N. (2016) · Molecular Ecology Resources · doi:10.1111/1755-0998.12610 · Cited by 22
“One promising avenue is hybridization target enrichment (Gnirke et al. 2009), a cornerstone of many projects that need to enrich for particular loci.”
BackgroundZhang, Y. C., Deng, S., Liang, D., & Zhang, P. (2019) · Molecular Ecology Resources · doi:10.1111/1755-0998.13026 · Cited by 22
“Sequence capture is a technique for data collection in ecological and evolutionary studies (Albert et al., 2007; Gnirke et al., 2009; Hodges et al., 2007; Mamanova et al., 2010).”
Advances in legume research in the genomics era
Egan, A. N., & Vatanparast, M. (2019) · Australian Systematic Botany · doi:10.1071/sb19019 · Cited by 22
Kihana, M., Mizuno, F., Sawafuji, R., Wang, L., & Ueda, S. (2013) · Gene · doi:10.1016/j.gene.2013.07.040 · Cited by 22
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Viso, F. D., Bhattacharya, D., Kong, Y., Gilchrist, M. J., & Khokha, M. K. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-649 · Cited by 21
“; licensee BioMed Centra Commons Attribution License (http://creativec reproduction in any medium, provided the or To perform exome sequencing, exons are captured using arrays [6-8] or in solution [9] with specifically designed probes.”
The Quest for Rare Variants: Pooled Multiplexed Next Generation Sequencing in Plants
Marroni, F., Pinosio, S., & Morgante, M. (2012) · Frontiers in Plant Science · doi:10.3389/fpls.2012.00133 · Cited by 21
“An alternative approach is the use of hybridization-based target enrichment methods (Gnirke et al., 2009), which can target regions from few to hundreds of megabases (the size of human exome).”
MethodGene mutation discovery research of non-smoking lung cancer patients due to indoor radon exposure
Choi, J. R., Park, S. Y., Noh, O. K., Koh, Y. W., & Kang, D. R. (2016) · Annals of Occupational and Environmental Medicine · doi:10.1186/s40557-016-0095-2 · Cited by 21
“PCR based NGS is an outstanding tool to provide a comprehensive genomic diagnosis in patients with recurrent LCINS [53].”
MethodPersonal Neoantigens From Patients With NSCLC Induce Efficient Antitumor Responses
Zhang, W., Yin, Q., Huang, H., Lu, J., Qin, H., Chen, S., Zhang, W., Su, X., Sun, W., Dong, Y., et al. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.628456 · Cited by 21
“Whole-exome capture was performed using an Agilent Sure Select Human All Exon 44- Mb version 2.0 bait set (Agilent Technologies) (21).”
InfluentialAiming off the target: recycling target capture sequencing reads for investigating repetitive DNA
Costa, L. G. A., Marques, A., Buddenhagen, C. E., Thomas, W. W., Hüettel, B., Schubert, V., Dodsworth, S., Houben, A., Souza, G., & Pedrosa‐Harand, A. (2021) · Annals of Botany · doi:10.1093/aob/mcab063 · Cited by 21
Epigenetic biomarkers for animal welfare monitoring
Whelan, R., Tönges, S., Böhl, F., & Lyko, F. (2023) · Frontiers in Veterinary Science · doi:10.3389/fvets.2022.1107843 · Cited by 23
“Similarly, it is possible to capture specific genomic regions of interest with biotinylated RNA oligonucleotide “baits” (44) before analyzing them by bisulfite sequencing.”
BackgroundMassively parallel DNA sequencing from routinely processed cytological smears
Piqueret‐Stephan, L., Marcaillou, C., Réyès, C., Honoré, A., Letexier, M., Gentien, D., Droin, N. M., Lacroix, L., Scoazec, J., & Vielh, P. R. (2015) · Cancer Cytopathology · doi:10.1002/cncy.21639 · Cited by 21
“Genomic DNA was captured with Agilent’s insolution enrichment methodology (SureSelect Human All Exon kit, version 5; Agilent Technologies) with the biotinylated oligonucleotide probe library (Human All Exon kit, version 5, 50 Mb; Agilent Technologies), and this was followed by paired-end, 75-base massively parallel se…”
MethodZuzarte, P. C., Denroche, R. E., Fehringer, G., Katzov-Eckert, H., Hung, R. J., & McPherson, J. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093455 · Cited by 21
“Pooled DNA was captured using custom probes and Agilent SureSelect technology [13] targeting a 250 kb region of chromosome 5 (5p15.”
MethodImputing gene expression from selectively reduced probe sets
Donner, Y., Feng, T., Benoist, C. O., & Koller, D. (2012) · Nature Methods · doi:10.1038/nmeth.2207 · Cited by 21
“An alternative approach 1,8,20,21 exploits redundancy to reduce costs by measuring a small subset of ‘signature probes’ cheaply using technologies such as bead assays 22 , reverse transcriptase– PCR 23,24 , direct multiplexed measurement 25 , microfluidic dynamic arrays 26 or hybrid selection 27 .”
BackgroundNext-generation sequencing: a frameshift in skeletal dysplasia gene discovery
Lazarus, S., Zankl, A., & Duncan, E. L. (2013) · Osteoporosis International · doi:10.1007/s00198-013-2443-1 · Cited by 21
Bisulfite Methylation Profiling of Large Genomes
Reinders, J., & Paszkowski, J. (2010) · Epigenomics · doi:10.2217/epi.10.6 · Cited by 22
Wood, J. R., & Pietri, V. L. D. (2015) · The Auk · doi:10.1642/auk-14-257.1 · Cited by 21
“New protocols also continue to be developed for increasing the efficiency of aDNA recovery from ancient specimens (e.g., Gnirke et al. 2009, Mertes et al. 2011, Gansauge and Meyer 2013), and in future such methods may potentially increase the temporal range of aDNA studies.”
BackgroundWhole exome sequencing for handedness in a large and highly consanguineous family
Kavaklioglu, T., Ajmal, M., Hameed, A., & Francks, C. (2015) · Neuropsychologia · doi:10.1016/j.neuropsychologia.2015.11.010 · Cited by 21
“A further possibility is that our exome capture and sequencing missed a putatively causal exomic variant for the trait, as the protocol that we used is known to miss between 5–10% of proteincoding DNA variation (Gnirke et al., 2009; SureSelect Performance, 2015).”
The impact of genomics on population genetics of parasitic diseases
Hupalo, D. N., Bradic, M., & Carlton, J. (2014) · Current Opinion in Microbiology · doi:10.1016/j.mib.2014.11.001 · Cited by 18
“A second new technology adopted by the parasite genomics community is “hybrid selection”, which uses biotinylated RNA baits designed from a parasite reference genome sequence to capture parasite DNA from a host-parasite DNA mixture [15].”
BackgroundMultiplex target capture with double-stranded DNA probes
Shen, P., Wang, W., Chi, A.-K., Fan, Y., Davis, R. W., & Scharfe, C. (2013) · Genome Medicine · doi:10.1186/gm454 · Cited by 21
“The most widely used methods utilize multiplex PCR amplification [6-8], hybrid-capture [9-12], selective target circularization [13-21], and oligonucleotide-selective sequencing [22].”
MethodGenomic selection prediction models comparing sequence capture and SNP array genotyping methods
de Moraes, B. F. X., dos Santos, R. F., de Lima, B. M., Aguiar, A. M., Missiaggia, A. A., Dias, D. D. C., Rezende, G. D. P. S., Gonçalves, F. M. A., Acosta, J. J., Kirst, M., et al. (2018) · Molecular Breeding · doi:10.1007/s11032-018-0865-3 · Cited by 21
Sanger Sequencing Principles, History, and Landmarks
Valencia, C. A., Pervaiz, M. A., Husami, A., Qian, Y., & Zhang, K. (2013) · SpringerBriefs in genetics · doi:10.1007/978-1-4614-9032-6_1 · Cited by 20
Solution-based targeted genomic enrichment for precious DNA samples
Shearer, A. E., Hildebrand, M. S., & Smith, R. J. (2012) · BMC Biotechnology · doi:10.1186/1472-6750-12-20 · Cited by 20
“TGE may be performed in solution (solution-based targeted genomic enrichment, solution-based TGE, [5]), or on an array platform (solid-phase targeted genomic enrichment, solid-phase TGE, [6]).”
BackgroundInfluentialFrom the Phenotype to the Genotype via Bioinformatics
Willet, C. E., & Wade, C. M. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0847-9_1 · Cited by 21
Novel CALM3 Variant Causing Calmodulinopathy With Variable Expressivity in a 4-Generation Family
Kato, K., Isbell, H. M., Fressart, V., Denjoy, I., Debbiche, A., Itoh, H., Poinsot, J., George, A. L., Coulombe, A., Shea, M. A., et al. (2022) · Circulation Arrhythmia and Electrophysiology · doi:10.1161/circep.121.010572 · Cited by 21
Ancient genomes reveal insights into ritual life at Chichén Itzá
Barquera, R., Chávez, O. D. C., Nägele, K., Pérez-Ramallo, P., Hernández-Zaragoza, D. I., Szolek, A., Rohrlach, A. B., Librado, P., Childebayeva, A., Bianco, R. A., et al. (2024) · Nature · doi:10.1038/s41586-024-07509-7 · Cited by 20
“Using an in-solution capture approach based on modified immortalized probe sequences 136 , target immunity genes sequences, mtDNA, Y chromosome or a panel of 1,237,207 SNPs were enriched from the total DNA in the sequencing libraries 32,33,137–140 .”
MethodBacher, U., Kohlmann, A., & Haferlach, T. (2010) · Cancer Treatment Reviews · doi:10.1016/j.ctrv.2010.05.002 · Cited by 21
Whole human exome capture for high-throughput sequencing
Kim, D.-W., Nam, S.-H., Kim, R. N., Choi, S.-H., & Park, H.-S. (2010) · Genome · doi:10.1139/g10-025 · Cited by 21
Molecular tools for companion diagnostics
Zieba, A., Grannas, K., Söderberg, O., Gullberg, M. T., Nilsson, M. F., & Landegren, U. D. (2012) · New Biotechnology · doi:10.1016/j.nbt.2012.05.004 · Cited by 20
Refinement of Molecular Diagnostic Protocol of Auditory Neuropathy Spectrum Disorder
Chang, M. Y., Kim, A. R., Kim, N. K. D., Lee, C., Park, W., & Choi, B. Y. (2015) · Medicine · doi:10.1097/md.0000000000001996 · Cited by 20
Universal Human Papillomavirus Typing Assay: Whole-Genome Sequencing following Target Enrichment
Li, T., Unger, E. R., Batra, D. G., Sheth, M., Steinau, M., Jasinski, J., Jones, J., & Rajeevan, M. S. (2017) · Journal of Clinical Microbiology · doi:10.1128/jcm.02132-16 · Cited by 20
“DNA/RNA baits were initially used and proved to be highly effective to enrich human exomes for variant calling by deep sequencing (20, 21).”
MethodPhylogeography of ants from the Brazilian Atlantic Forest
Ströher, P. R., Meyer, A. L. S., Zarza, E., Tsai, W. L. E., McCormack, J. E., & Pie, M. R. (2019) · Organisms Diversity & Evolution · doi:10.1007/s13127-019-00409-z · Cited by 20
Choo, L. Q., Bal, T. M. P., Choquet, M., Smolina, I., Ramos‐Silva, P., Marlétaz, F., Kopp, M., Hoarau, G. G., & Peijnenburg, K. T. C. A. (2020) · BMC Genomics · doi:10.1186/s12864-019-6372-z · Cited by 20
Schultzhaus, Z. S., Wang, Z., & Stenger, D. A. (2020) · Diagnostic Microbiology and Infectious Disease · doi:10.1016/j.diagmicrobio.2020.115275 · Cited by 20
Forensic DNA profiling: state of the art
Linacre, A. M. T., & Templeton, J. E. L. (2014) · Research and Reports in Forensic Medical Science · doi:10.2147/rrfms.s60955 · Cited by 22
Targeted sequencing with microfluidics
Kirkness, E. F. (2009) · Nature Biotechnology · doi:10.1038/nbt1109-998 · Cited by 20
Smith, M., Campino, S., Gu, Y., Clark, T., Otto, T., Maslen, G., Manske, M., Imwong, M., Dondorp, A., Kwiatkowski, D., et al. (2012) · The Open Genomics Journal · doi:10.2174/1875693x01205010018 · Cited by 18
Integrated genomic analyses of ovarian carcinoma
The Cancer Genome Atlas Research Network (2011) · Nature · doi:10.1038/nature10166 · Cited by 129
The Degradation of dG Phosphoramidites in Solution
Hargreaves, J. S., Kaiser, R., & Wolber, P. K. (2015) · Nucleosides Nucleotides & Nucleic Acids · doi:10.1080/15257770.2015.1071846 · Cited by 19
“, 100 bases and longer), which are important components of some microarrays and many sequencing target enrichment products,[9] take many hours to synthesize.”
BackgroundMethodNepomnyashchaya, Y. N., Artemov, A. V., Roumiantsev, S. A., Roumiantsev, A. G., & Zhavoronkov, A. A. (2012) · Clinical Chemistry and Laboratory Medicine (CCLM) · doi:10.1515/cclm-2012-0281 · Cited by 20
“successfully performed a 213-fold enrichment of the selected loci of cfDNA from the blood samples of pregnant women [35] as an example of an in-solution, separation-based enrichment technique [34] .”
MethodDetection of Genomic Variation by Selection of a 9 Mb DNA Region and High Throughput Sequencing
Nikolaev, S. I., Iseli, C., Sharp, A. J., Robyr, D., Rougemont, J., Gehrig, C., Farinelli, L., & Antonarakis, S. E. (2009) · PLoS ONE · doi:10.1371/journal.pone.0006659 · Cited by 19
Robertson, F. M., Shaw, R., & Macqueen, D. J. (2016) · Marine Genomics · doi:10.1016/j.margen.2016.06.003 · Cited by 21
“An alternative approach has been to exploit custom-designed microarrays or solutionbased hybridization platforms to enrich for sequences (i.e. sequence capture) prior to second-generation sequencing (e.g. Okou et al., 2007; Gnirke et al., 2009; Turner et al., 2009).”
MethodWu, C., Yin, Y., Zhu, L.-L., Zhang, Y., & Li, Y. (2021) · Drug Discovery Today · doi:10.1016/j.drudis.2021.11.008 · Cited by 19
Li, X., Liu, X., Fan, Y., Li, S., Yu, M., Qian, M., Chen, Y., Chen, H., Li, X., Liu, B., et al. (2022) · The Crop Journal · doi:10.1016/j.cj.2022.08.008 · Cited by 19
Solomon, B. D., Pineda‐Alvarez, D., Hadley, D. W., Hansen, N. F., Kamat, A., Donovan, F. X., Chandrasekharappa, S. C., Hong, S., Roessler, E., Mullikin, J. C., et al. (2012) · Molecular Syndromology · doi:10.1159/000345406 · Cited by 19
“, USA), using biotinylated RNA baits to hybridize to sequences corresponding to exons [Gnirke et al., 2009].”
MethodA comparison of whole genome sequencing with exome sequencing for family-based association studies
Lacey, S., Chung, J., & Lin, H. (2014) · BMC Proceedings · doi:10.1186/1753-6561-8-s1-s38 · Cited by 19
“Several commercial exome-capture platforms are currently available, each with a different design focus [4-6].”
BackgroundA regression model for estimating DNA copy number applied to capture sequencing data
Rigaill, G. J., Cadot, S., Kluin, R. J. C., Xue, Z., Bernards, R., Majewski, I. J., & Wessels, L. F. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts448 · Cited by 19
“Using the outcome of this model, we segment the data into regions where the proportionality between the test coverage and control coverage is constant, which should equate to regions with similar copy number.”
BackgroundMethodA method for positive forensic identification of samples from extremely low-coverage sequence data
Vohr, S. H., Najar, C. F. B. A., Shapiro, B., & Green, R. E. (2015) · BMC Genomics · doi:10.1186/s12864-015-2241-6 · Cited by 18
“Deep sequencing and capture techniques [8–11] can be applied to recover more human DNA from each sample but, ultimately, the total amount of useful human DNA sequence is limited by the number of intact human DNA fragments in the sample.”
BackgroundPeng, Z., Fan, W., Wang, L., Paudel, D., Leventini, D., Tillman, B. L., & Wang, J. (2017) · Molecular Genetics and Genomics · doi:10.1007/s00438-017-1327-z · Cited by 21
Huang, Z., Kelly, S., Matsuo, R., Li, L., Li, Y., Olsen, K. M., Jia, Y., & Caicedo, A. L. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200605 · Cited by 19
Ferreira, P. D. L., Batista, R., Andermann, T., Groppo, M., Bacon, C. D., & Antonelli, A. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107432 · Cited by 19
Wendt, F. R., Zeng, X., Churchill, J. D., King, J. L., & Budowle, B. (2016) · American Journal of Forensic Medicine & Pathology · doi:10.1097/paf.0000000000000228 · Cited by 19
Tracing the evolution of sequencing into the era of genomic medicine
Mardis, E. R., & Wilson, R. K. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-025-00884-5 · Cited by 18
Technological advances in DNA sequence enrichment and sequencing for germline genetic diagnosis
Ku, C., Wu, M., Cooper, D. N., Naidoo, N., Yudi Pawitan, Y., Pang, B., Iacopetta, B. J., & Soong, R. (2012) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.11.95 · Cited by 18
Genomics and epigenomics: new promises of personalized medicine for cancer patients
Schweiger, M. R., Barmeyer, C., & Timmermann, B. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt024 · Cited by 19
“niques to reduce DNA sequence complexities have been established [12–16].”
Enrichment of low abundance DNA/RNA by oligonucleotide-clicked iron oxide nanoparticles
Damavandi, F., Wang, W., Shen, W., Çetinel, S., Jordan, T., Jovel, J., Montemagno, C. D., & Wong, G. K. (2021) · Scientific Reports · doi:10.1038/s41598-021-92376-9 · Cited by 18
Metadata
- Authors
- Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., Brockman, W., Fennell, T., Giannoukos, G., Fisher, S., Russ, C., Gabriel, S., Jaffe, D. B., Lander, E. S., & Nusbaum, C.
- Affiliations
- Broad Institute (US)
- Agilent Technologies (United States) (US)
- Corresponding author
- Gnirke, Andreas
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2009-02
- Volume
- 27
- Issue
- 2
- Pages
- 182-189
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC2663421
- OpenAlex
- W2121531763
- Cited by
- 1,433
- References
- 25
- Citations by year
- 2026: 23 · 2025: 48 · 2024: 70 · 2023: 54 · 2022: 56 · 2021: 64 · 2020: 67 · 2019: 70 · 2018: 86 · 2017: 85 · 2016: 105 · 2015: 108 · 2014: 105 · 2013: 110 · 2012: 130
- FWCI
- 51.05
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Biotechnology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Broad Institute
- National Human Genome Research Institute (U54HG003067, HG03067-05)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- targeted sequencing, DNA capture, exon capture, next-generation sequencing, genotype calling, human genome
- MeSH terms
- Base Composition, Bayes Theorem, Exons, Humans, Nucleic Acid Hybridization, Oligonucleotides, Sensitivity and Specificity, Reproducibility of Results, Polymerase Chain Reaction, Sequence Analysis, DNA, Biotinylation, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genomics
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